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alphafold

Open source code for AlphaFold.

auto_autodock-gpu

Tools that help high-throughput protein-ligand docking in batch mode using AutoDock-GPU.

autodock-gpu

AutoDock for GPUs using OpenCL

autodocktools_py3

Python3 translation of AutoDockTools

awesome-chemistry-datasets

overview of datasets for ML in chemistry

awesome-legal

Awesome free legal documents for companies

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

chemfilter

Desktop app for using Transformer-CNN ADMETox models

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

diffsbdd

A Euclidean diffusion model for structure-based drug design.

etoxpred

A simple tool to predict the general toxicity and calculate the synthesize accessibility (SA) score for small molecules.

fast-nw-and-sw-pairwise-alignment-using-numba-jit

This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

glycosylator

Framework for the rapid modeling glycans and glycoproteins.

gpmodel

Functions and classes for doing Gaussian process models of proteins

grover

This is a Pytorch implementation of the paper: Self-Supervised Graph Transformer on Large-Scale Molecular Data

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

models

Trained caffe models

moleculartransformerembeddings

Code and data for the Transformer neural network trained to translate between molecular text representations and create molecular embeddings.

molformer

Repository for MolFormer

openmm-pmf

Code for computing PMFs. Directly used to compute ion diffusion barriers through pores in graphene sheets.

predictf

promotech

Machine-learning-based general bacterial promoter prediction tool.

segment-anything-with-webcam-in-real-time-with-fastsam

Segment Anything with Webcam in Real-Time with FastSAM

slurm-gcp

Slurm on Google Cloud Platform

tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

transdti

TransDTI: Transformer-based language models for estimating DTIs and building a drug-recommendation workflow

transvae

A Transformer Based VAE Architecture for De Novo Molecular Design

vina-gpu

A heterogeneous OpenCL implementation of AutoDock Vina